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# Snakemake workflow for full reproducibility of the project | ||
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## Description | ||
## Usage | ||
Run | ||
`snakemake --configfile config/config.yaml --cores 4 --use-conda` | ||
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To run the workflow, run `snakemake` | ||
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If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above). | ||
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Owner: Johannes Gawron |
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repos: | ||
- repo: https://github.com/snakemake/snakefmt | ||
rev: v0.10.2 # Replace by any tag/version ≥0.2.4 : https://github.com/snakemake/snakefmt/releases | ||
hooks: | ||
- id: snakefmt |
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sample: ['Br11', 'Br7', 'Br61', 'Br38', 'LM2', 'Pr9', 'Br23','Br39', 'Br57', 'Lu2', 'Br16_AC', 'Br16_B', 'Br16_C', 'Br26', 'Br44', 'Lu7', 'Br30', 'Br45', 'Ov8', 'Br37', 'Br46', 'Brx50', 'Pr6'] | ||
author: Johannes Gawron |
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from pathlib import Path | ||
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SAMPLES = config['sample'] | ||
PROJECT_DIR = Path(workflow.basedir).parent | ||
SCRIPT_DIR = Path(workflow.basedir) / 'scripts' | ||
RESOURCES_DIR = Path(workflow.basedir) / 'resources' | ||
markdown_helper_functions = (RESOURCES_DIR / 'functions.R').resolve().as_posix().replace('/', '\\/') | ||
print(markdown_helper_functions) | ||
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######Rules###### | ||
include: 'rules/base.smk' | ||
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all_files = [] | ||
for sample in SAMPLES: | ||
all_files.append((PROJECT_DIR / 'data' / 'htmls' / f'{sample}.html').resolve()) | ||
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rule all: | ||
input: | ||
all_files |
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channels: | ||
- conda-forge | ||
- bioconda | ||
- r | ||
- defaults | ||
dependencies: | ||
- r>=4.3 | ||
- r-rcpp>=1.0 | ||
- r-tidyverse>=2.0 | ||
- pandoc>=3.1 |